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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

2vn1

2.350 Å

X-ray

2008-01-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Peptidylprolyl isomerase
ID:Q8I4V8_PLAF7
AC:Q8I4V8
Organism:Plasmodium falciparum
Reign:Eukaryota
TaxID:36329
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A60 %
B40 %


Ligand binding site composition:

B-Factor:27.993
Number of residues:45
Including
Standard Amino Acids: 43
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0911471.500

% Hydrophobic% Polar
45.8754.13
According to VolSite

Ligand :
2vn1_1 Structure
HET Code: FK5
Formula: C44H69NO12
Molecular weight: 804.018 g/mol
DrugBank ID: DB00864
Buried Surface Area:65.85 %
Polar Surface area: 178.36 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 3
Rings: 4
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 7

Mass center Coordinates

XYZ
0.053789532.863815.1557


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C37CD1LEU- 233.890Hydrophobic
C5CZTYR- 4440Hydrophobic
C34CG2VAL- 454.260Hydrophobic
C23CG2VAL- 454.10Hydrophobic
C35CE1PHE- 554.240Hydrophobic
O6OD2ASP- 562.69157.76H-Bond
(Ligand Donor)
C33CBSER- 573.590Hydrophobic
C29CBPHE- 594.150Hydrophobic
C31CBPHE- 594.110Hydrophobic
C33CBPHE- 594.210Hydrophobic
C42CD1PHE- 593.70Hydrophobic
C43CZPHE- 593.840Hydrophobic
C17CE1PHE- 654.020Hydrophobic
C36CD1PHE- 653.760Hydrophobic
C41CE1PHE- 653.640Hydrophobic
C4CE2PHE- 653.480Hydrophobic
O10OGLU- 732.62131.15H-Bond
(Ligand Donor)
C3CBVAL- 744.40Hydrophobic
C4CG1VAL- 744.140Hydrophobic
C3CG1ILE- 754.130Hydrophobic
C30CG2ILE- 754.060Hydrophobic
O2NILE- 753.14150.56H-Bond
(Protein Donor)
C5CZ2TRP- 783.860Hydrophobic
C3CE2TRP- 783.430Hydrophobic
C18CDLYS- 903.970Hydrophobic
C38CDLYS- 904.20Hydrophobic
C30CE1TYR- 1014.030Hydrophobic
C35CZTYR- 1014.280Hydrophobic
C42CE1TYR- 10140Hydrophobic
O3OHTYR- 1012.75174.62H-Bond
(Protein Donor)
C12SGCYS- 1064.440Hydrophobic
C35SGCYS- 1063.940Hydrophobic
C35CD1ILE- 1103.610Hydrophobic
C38CBGLU- 1214.080Hydrophobic
O10OHOH- 20622.69179.99H-Bond
(Protein Donor)